MCMCvis, created by lab PhD candidate Casey Youngflesh is now peer reviewed and published in the Journal of Open Source Software! JOSS is journal that focuses exclusively on scientific software. While I think most would agree that giving software developers credit for their work is important, I think the practice of citing R packages (at least in ecology) is relatively rare. I (Casey) myself am guilty of this, to be sure. Cite the R packages/other software you use – publications and citations of those pubs are the currency of academia!
Lab PhD candidate, Catherine Foley has a great piece out in Earthzine this week about the importance of sea ice to polar ecosystems and how scientists use satellites to study it. Check it out!
Lynch Lab High School student, Reid Biondo’s work was highlighted in The Port Times Record this week! Reid was working on using Convolutional Neural Networks to classify Antarctic Seals.
- R-hat (AKA Gelman-Rubin statistic) – used to assess convergence of chains in the model
- Visual assessment of chains – used to assess whether posterior chains mixed well (convergence)
- Visual assessment of posterior distribution shape – used to determine if the posterior distribution is constrained
- Posterior predictive check (predicting data using estimated parameters) – used to make sure that the model can generate the data used in the model
One check, however, is often missing: a robust assessment of the degree to which the prior is informing the posterior distribution. Substantial influence of the prior on the posterior may not be apparent through the use of R-hat and visual checks alone. Version 0.9.2 of
MCMCvis (now available on CRAN), makes quantifying and plotting the prior posterior overlap (PPO) simple.
MCMCvis is an R package designed to streamline analysis of Bayesian model results derived from MCMC samplers (e.g., JAGS, BUGS, Stan). It can be used to easily visualize, manipulate, and summarize MCMC output. The newest version is full of new features – a full tutorial can be found here.
To check PPO for a model, we will use the function
MCMCtrace. As the function is used to generate trace and density plots, checking for PPO is barely more work than just doing the routine checks that one would ordinarily perform. The function plots trace plots on the left and density plots for both the posterior (black) and prior (red) distributions on the right. The function calculates the percent overlap between the prior and posterior and prints this value on the plot. See
?MCMCtrace in R for details regarding the syntax.
#install package install.packages('MCMCvis', repos = "http://cran.case.edu") #load package require(MCMCvis) #load example data data(MCMC_data) #simulate data from the prior used in your model #number of iterations should equal the number of draws times the number of chains (although the function will adjust if the correct number of iterations is not specified) #in JAGS: parameter ~ dnorm(0, 0.001) PR <- rnorm(15000, 0, 32) #run the function for just beta parameters MCMCtrace(MCMC_data, params = 'beta', priors = PR, pdf = FALSE)
Checking the PPO has particular utility when trying to determine if the parameters in your model are identifiable. If substantial PPO exists, the prior may simply be dictating the posterior distribution – the data may have little influence on the results. If a small degree of PPO exists, the data was informative enough to overcome the influence of the prior. In the field of ecology, nonidentifiability is a particular concern in some types of mark-recapture models. Gimenez (2009) developed quantitative guidelines to determine when parameters are robustly identifiable using PPO.
While a large degree of PPO is not always a bad thing (e.g., substantial prior knowledge about the system may result in very informative priors used in the model), it is important to know where data was and was not informative for parameter estimation. The degree of PPO that is acceptable for a particular model will depend on a great number of factors, and may be somewhat subjective (but see Gimenez  for a less subjective case). Like other checks, PPO is just one of many tools to be used for model assessment. Finding substantial PPO when unexpected may suggest that further model manipulation is needed. Happy model building!
Check out the rest of the new package freatures, including the option to calculate the number of effective samples for each parameter, ability to take arguments in the form of a ‘regular expression’ for the
params argument, ability to retain the structure of all parameters in model output (e.g., parameters specified as matrices in the model are summarized as matrices).
The study, led by Lynch Lab postdoc Chris Che-Castaldo, highlights the need to aggregate abundance estimates over space to produce robust estimates of abundance when substantial stochasticity exists in populations. Adélie penguin population dynamics are inherently noisy, making it difficult to separate signal from noise when using these birds as indicators for environmental change. Nearly the entire global population of Adélie penguins was modeled in this effort, using every piece of publicly available data on Adélie penguin abundance. All code and data (instructions on how to query the database) to run the analyses available in the supplements! Check out the MAPPPD website to interact with the model results and check out penguin population dynamics for yourself.
Congratulations to Bento Goncalves, who was recently announced as one of the 2017 IACS Jr. Research Award Winners. This award will help support Bento’s thesis research on using ‘deep learning’ for pack ice seal surveys. Congratulations as well to Catie Foley, who was one of the winners of the 1st Annual STRIDE visualization contest. Nice work!
This week, six undergraduates from the Lynch Lab presented their research at Stony Brook’s Undergraduate Research & Creative Activities (URECA) Symposium:
Adaptive Significance of King Penguin (Aptenodytes patagonicus) Crèches
Lisa Caligiuri, Catherine Foley, and Heather Lynch
Variation in Population Dynamics of King Penguins, Aptenodytes patagonicus, Across Phylogenetic and Regional Scales
Vanessa Kennelly, Maureen Lynch, Catherine Foley, and Heather Lynch
Variation in the ecstatic display call of the gentoo penguin (Pygoscelis papua) associated with behavioral responses
Medha Pandey, Maureen Lynch, and Heather Lynch
Climate indices explain variation in fur seal pup mortality
Katla Thorsen, Casey Youngflesh, and Heather Lynch
The Effect of Oceanographic Conditions on Pygoscelis Penguin Population Dynamics
Arianna West, Catherine Foley, Heather Lynch
Phylogenetic Relationships between Conservation Risk and Life History Traits in Seabirds
Helen Wong, Maureen Lynch, Heather Lynch
Congratulations to each of these outstanding students!
The Lynch Lab is proud to announce that Sara Vincent, an undergraduate student working in the lab, has been awarded Stony Brook’s 2017 Undergraduate Research and Creative Activities (URECA) Biology Alumni Research Award. With the receipt of this award, Sara will spend the summer in the lab working on her independent project examining the spatial patterns of elephant seal harems.
A recent study on Adélie penguin phenology, led by Lynch Lab Ph.D. candidate Casey Youngflesh, is featured as the cover story in this month’s issue of Ecology. This study highlights some, heretofore, unappreciated nuances of phenological mismatch and advances our understanding of phenology and mismatch in highly variable systems. Freely available copy here!